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Yorodumi- PDB-3pvi: D34G MUTANT OF PVUII ENDONUCLEASE COMPLEXED WITH COGNATE DNA SHOW... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3pvi | ||||||
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Title | D34G MUTANT OF PVUII ENDONUCLEASE COMPLEXED WITH COGNATE DNA SHOWS THAT ASP34 IS DIRECTLY INVOLVED IN DNA RECOGNITION AND INDIRECTLY INVOLVED IN CATALYSIS | ||||||
Components |
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Keywords | HYDROLASE/DNA / COMPLEX (RESTRICTION ENDONUCLEASE-DNA) / MUTANT / PROTEIN/DNA / HYDROLASE-DNA COMPLEX | ||||||
Function / homology | Function and homology information type II site-specific deoxyribonuclease / type II site-specific deoxyribonuclease activity / DNA restriction-modification system / DNA binding / metal ion binding Similarity search - Function | ||||||
Biological species | Proteus vulgaris (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 1.59 Å | ||||||
Authors | Horton, J.R. / Cheng, X. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 1998 Title: Asp34 of PvuII endonuclease is directly involved in DNA minor groove recognition and indirectly involved in catalysis. Authors: Horton, J.R. / Nastri, H.G. / Riggs, P.D. / Cheng, X. #1: Journal: Embo J. / Year: 1994 Title: Structure of PvuII Endonuclease with Cognate DNA Authors: Cheng, X. / Balendiran, K. / Schildkraut, I. / Anderson, J.E. #2: Journal: Proteins / Year: 1994 Title: Expression, Purification, and Crystallization of Restriction Endonuclease PvuII with DNA Containing its Recognition Site Authors: Balendiran, K. / Bonventre, J. / Knott, R. / Jack, W. / Benner, J. / Schildkraut, I. / Anderson, J.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3pvi.cif.gz | 98.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3pvi.ent.gz | 72.4 KB | Display | PDB format |
PDBx/mmJSON format | 3pvi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pv/3pvi ftp://data.pdbj.org/pub/pdb/validation_reports/pv/3pvi | HTTPS FTP |
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-Related structure data
Related structure data | 1pviS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: DNA chain | Mass: 3967.585 Da / Num. of mol.: 2 / Source method: obtained synthetically #2: Protein | Mass: 18312.957 Da / Num. of mol.: 2 / Mutation: D34G Source method: isolated from a genetically manipulated source Source: (gene. exp.) Proteus vulgaris (bacteria) / Plasmid: PBBE3 / Production host: Escherichia coli (E. coli) / Strain (production host): PR653 / References: UniProt: P23657 #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.23 Å3/Da / Density % sol: 52 % | |||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 4.5 / Details: pH 4.5 | |||||||||||||||||||||||||||||||||||||||||||||
Crystal | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 16 ℃ / Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X12B / Wavelength: 1.14 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Details: COLLIMATOR |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.14 Å / Relative weight: 1 |
Reflection | Resolution: 1.59→40 Å / Num. obs: 52374 / % possible obs: 98.5 % / Observed criterion σ(I): 0 / Redundancy: 5.75 % / Rmerge(I) obs: 0.038 |
Reflection shell | Resolution: 1.59→1.66 Å / Rsym value: 0.317 / % possible all: 69 |
Reflection | *PLUS Num. measured all: 301390 |
-Processing
Software |
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Refinement | Method to determine structure: OTHER Starting model: PDB ENTRY 1PVI Resolution: 1.59→5 Å / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / σ(F): 0
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Displacement parameters | Biso mean: 23 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.59→5 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.59→1.66 Å / Total num. of bins used: 8 /
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Xplor file |
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 5 Å / % reflection Rfree: 10 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 23 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | *PLUS Rfactor Rfree: 0.345 / % reflection Rfree: 10 % / Rfactor Rwork: 0.317 |